Andal.LND/edx-platform
6
0
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases Wiki Activity

miller indices calculation

Browse Source
This commit is contained in:
Александр
2012-11-21 17:53:51 +02:00
parent aaeffa5316
commit d5dd725537
1 changed files with 124 additions and 52 deletions
Download Patch File Download Diff File Expand all files Collapse all files

176
common/lib/capa/capa/chem/miller.py
View File

@@ -1,12 +1,9 @@
# 1) Calculate miller indices by points coordinates
# 2) Grader for miller indeces and lattice type
import numpy as np
import math
import fractions as fr
import decimal
import unittest
import json
def lcm(a, b):
@@ -27,7 +24,8 @@ def section_to_fraction(distance):
return fr.Fraction(1, 1) # ERROR, need shift of coordinates
else:
# limit_denominator to closest nicest fraction
fract = fr.Fraction(distance).limit_denominator() # 5 / 2 : numerator / denominator
# import ipdb; ipdb.set_trace()
fract = fr.Fraction(distance).limit_denominator(10) # 5 / 2 : numerator / denominator
print 'Distance', distance, 'Inverted fraction', fract
# return inverted fraction
return fr.Fraction(fract.denominator, fract.numerator)
@@ -50,7 +48,9 @@ def sub_miller(sections):
# import ipdb; ipdb.set_trace()
# nice output:
output = '(' + ''.join(map(str, map(decimal.Decimal, miller))) + ')'
# output = '(' + ''.join(map(str, map(decimal.Decimal, miller))) + ')'
# import ipdb; ipdb.set_trace()
output = '(' + ','.join(map(str, map(decimal.Decimal, miller))) + ')'
print 'Miller indices:', output
return output
@@ -59,11 +59,11 @@ def miller(points):
"""Calculate miller indices of plane
"""
print "\nCalculating miller indices:"
print 'Points:\n', points
# print "\nCalculating miller indices:"
# print 'Points:\n', points
# calculate normal to plane
N = np.cross(points[1] - points[0], points[2] - points[0])
print "Normal:", N
# print "Normal:", N
# origin
O = np.array([0, 0, 0])
@@ -116,73 +116,146 @@ def miller(points):
return sub_miller(sections)
class Test_Crystallography_Grader(unittest.TestCase):
def grade(user_input, correct_answer):
'''
Format:
user_input: {"lattice":"sc","points":[["0.77","0.00","1.00"],["0.78","1.00","0.00"],["0.00","1.00","0.72"]]}
"lattice" is one of: "", "sc", "bcc", "fcc"
correct_answer: {'miller': '(00-1)', 'lattice': 'bcc'}
'''
def negative(s):
# import ipdb; ipdb.set_trace()
output = ''
i = 1
while i in range(1, len(s) - 1):
if s[i] in (',', ' '):
output += s[i]
elif s[i] not in ('-', '0'):
output += '-' + s[i]
elif s[i] == '0':
output += s[i]
else:
i += 1
output += s[i]
i += 1
# import ipdb; ipdb.set_trace()
return '(' + output + ')'
user_answer = json.loads(user_input)
if user_answer['lattice'] != correct_answer['lattice']:
return False
points = [map(float, p) for p in user_answer['points']]
points = [np.array(point) for point in points]
# import ipdb; ipdb.set_trace()
print miller(points), (correct_answer['miller'].replace(' ', ''), negative(correct_answer['miller']).replace(' ', ''))
if miller(points) in (correct_answer['miller'].replace(' ', ''), negative(correct_answer['miller']).replace(' ', '')):
return True
return False
class Test_Crystallography_Miller(unittest.TestCase):
''' test crystallography grade function '''
def test_1(self):
x = np.array([0.5, 0, 0])
y = np.array([0, 0.5, 0])
z = np.array([0, 0, 0.5])
self.assertEqual(miller(np.array([x, y, z])), '(222)')
user_input = '{"lattice": "bcc", "points": [["0.50", "0.00", "0.00"], ["0.00", "0.50", "0.00"], ["0.00", "0.00", "0.50"]]}'
self.assertTrue(grade(user_input, {'miller': '(2,2,2)', 'lattice': 'bcc'}))
def test_2(self):
x = np.array([1, 0, 0])
y = np.array([0, 1, 0])
z = np.array([0, 0, 1])
self.assertEqual(miller(np.array([x, y, z])), '(111)')
user_input = '{"lattice": "bcc", "points": [["1.00", "0.00", "0.00"], ["0.00", "1.00", "0.00"], ["0.00", "0.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(1,1,1)', 'lattice': 'bcc'}))
def test_3(self):
x = np.array([1, 0.5, 1])
y = np.array([1, 1, 0.5])
z = np.array([0.5, 1, 1])
self.assertEqual(miller(np.array([x, y, z])), '(222)')
user_input = '{"lattice": "bcc", "points": [["1.00", "0.50", "1.00"], ["1.00", "1.00", "0.50"], ["0.50", "1.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(2,2,2)', 'lattice': 'bcc'}))
def test_4(self):
x = np.array([1. / 3, 1., 0])
y = np.array([0, 2. / 3., 0])
z = np.array([0, 1, 1. / 3])
self.assertEqual(miller(np.array([x, y, z])), '(-33-3)')
user_input = '{"lattice": "bcc", "points": [["0.33", "1.00", "0.00"], ["0.00", "0.664", "0.00"], ["0.00", "1.00", "0.33"]]}'
self.assertTrue(grade(user_input, {'miller': '(-3, 3, -3)', 'lattice': 'bcc'}))
def test_5(self):
x = np.array([1. / 3, 1., 0])
y = np.array([0, 1. / 3., 0])
z = np.array([0, 1, 1. / 3])
self.assertEqual(miller(np.array([x, y, z])), '(-63-6)')
user_input = '{"lattice": "bcc", "points": [["0.33", "1.00", "0.00"], ["0.00", "0.33", "0.00"], ["0.00", "1.00", "0.33"]]}'
self.assertTrue(grade(user_input, {'miller': '(-6,3,-6)', 'lattice': 'bcc'}))
def test_6(self):
x = np.array([0, 1. / 4., 0])
y = np.array([1. / 4, 0, 0])
z = np.array([0, 0, 1. / 4])
self.assertEqual(miller(np.array([x, y, z])), '(444)')
user_input = '{"lattice": "bcc", "points": [["0.00", "0.25", "0.00"], ["0.25", "0.00", "0.00"], ["0.00", "0.00", "0.25"]]}'
self.assertTrue(grade(user_input, {'miller': '(4,4,4)', 'lattice': 'bcc'}))
def test_7(self): # goes throug origin
x = np.array([0, 1., 0])
y = np.array([1., 0, 0])
z = np.array([0.5, 1., 0])
self.assertEqual(miller(np.array([x, y, z])), '(00-1)')
user_input = '{"lattice": "bcc", "points": [["0.00", "1.00", "0.00"], ["1.00", "0.00", "0.00"], ["0.50", "1.00", "0.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(0,0,-1)', 'lattice': 'bcc'}))
def test_8(self):
x = np.array([0, 1., 0.5])
y = np.array([1., 0, 0.5])
z = np.array([0.5, 1., 0.5])
self.assertEqual(miller(np.array([x, y, z])), '(002)')
user_input = '{"lattice": "bcc", "points": [["0.00", "1.00", "0.50"], ["1.00", "0.00", "0.50"], ["0.50", "1.00", "0.50"]]}'
self.assertTrue(grade(user_input, {'miller': '(0,0,2)', 'lattice': 'bcc'}))
def test_9(self):
x = np.array([0, 1. / 4., 0])
y = np.array([1. / 4, 0, 0])
z = np.array([0, 0, 1. / 4])
self.assertEqual(miller(np.array([x, y, z])), '(444)')
user_input = '{"lattice": "bcc", "points": [["1.00", "0.00", "1.00"], ["0.00", "1.00", "1.00"], ["1.00", "0.00", "0.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(1,1,0)', 'lattice': 'bcc'}))
def test_10(self):
x = np.array([0, 1. / 4., 0])
y = np.array([1. / 4, 0, 0])
z = np.array([0, 0, 1. / 4])
self.assertEqual(miller(np.array([x, y, z])), '(444)')
user_input = '{"lattice": "bcc", "points": [["1.00", "0.00", "1.00"], ["0.00", "0.00", "0.00"], ["0.00", "1.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(1,1,-1)', 'lattice': 'bcc'}))
def test_11(self):
user_input = '{"lattice": "bcc", "points": [["1.00", "0.00", "0.50"], ["1.00", "1.00", "0.00"], ["0.00", "1.00", "0.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(0,1,2)', 'lattice': 'bcc'}))
def test_12(self):
user_input = '{"lattice": "bcc", "points": [["1.00", "0.00", "0.50"], ["0.00", "0.00", "0.50"], ["1.00", "1.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(0,1,-2)', 'lattice': 'bcc'}))
def test_13(self):
user_input = '{"lattice": "bcc", "points": [["0.50", "0.00", "0.00"], ["0.50", "1.00", "0.00"], ["0.00", "0.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(2,0,1)', 'lattice': 'bcc'}))
def test_14(self):
user_input = '{"lattice": "bcc", "points": [["0.00", "0.00", "0.00"], ["0.00", "0.00", "1.00"], ["0.50", "1.00", "0.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(2,-1,0)', 'lattice': 'bcc'}))
def test_15(self):
user_input = '{"lattice": "bcc", "points": [["0.00", "0.00", "0.00"], ["1.00", "1.00", "0.00"], ["0.00", "1.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(1,-1,1)', 'lattice': 'bcc'}))
def test_16(self):
user_input = '{"lattice": "bcc", "points": [["1.00", "0.00", "0.00"], ["0.00", "1.00", "0.00"], ["1.00", "1.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(1,1,-1)', 'lattice': 'bcc'}))
def test_17(self):
user_input = '{"lattice": "bcc", "points": [["0.00", "0.00", "0.00"], ["1.00", "0.00", "1.00"], ["1.00", "1.00", "0.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(-1,1,1)', 'lattice': 'bcc'}))
def test_18(self):
user_input = '{"lattice": "bcc", "points": [["0.00", "0.00", "0.00"], ["1.00", "1.00", "0.00"], ["0.00", "1.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(1,-1,1)', 'lattice': 'bcc'}))
def test_19(self):
user_input = '{"lattice": "bcc", "points": [["0.00", "0.00", "0.00"], ["1.00", "1.00", "0.00"], ["0.00", "0.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(-1,1,0)', 'lattice': 'bcc'}))
def test_20(self):
user_input = '{"lattice": "bcc", "points": [["1.00", "0.00", "0.00"], ["1.00", "1.00", "0.00"], ["0.00", "0.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(1,0,1)', 'lattice': 'bcc'}))
def test_21(self):
user_input = '{"lattice": "bcc", "points": [["0.00", "0.00", "0.00"], ["0.00", "1.00", "0.00"], ["1.00", "0.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(-1,0,1)', 'lattice': 'bcc'}))
def test_22(self):
user_input = '{"lattice": "bcc", "points": [["0.00", "1.00", "0.00"], ["1.00", "1.00", "0.00"], ["0.00", "0.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(0,1,1)', 'lattice': 'bcc'}))
def test_23(self):
user_input = '{"lattice": "bcc", "points": [["0.00", "0.00", "0.00"], ["1.00", "0.00", "0.00"], ["1.00", "1.00", "1.00"]]}'
self.assertTrue(grade(user_input, {'miller': '(0,-1,1)', 'lattice': 'bcc'}))
def suite():
testcases = [Test_Crystallography_Grader]
testcases = [Test_Crystallography_Miller]
suites = []
for testcase in testcases:
suites.append(unittest.TestLoader().loadTestsFromTestCase(testcase))
@@ -190,4 +263,3 @@ def suite():
if __name__ == "__main__":
unittest.TextTestRunner(verbosity=2).run(suite())